The Betrayal
by protector91
Summary: Desperate to get the nano-mites out of her body, Ana hopes to free the Cobra-Commander, endangering the entire world. Determined to stop her Duke makes a decision he'll come to regret.
1. Betrayed

****

A/N: This is my very first G.I. Joe story.

"So you remember you have a brother," Rex said to Ana from inside his cell. Ana opened her mouth to speak, but Rex cut her off. "Let me guess, you don't have a brother anymore. Or maybe you were going to say your brother is dead."

"Shut up Commander," She said to him. "I'm only here because," "You want me to reveal how to get the nano-mites out of your body. Am I correct?"

"Yes."

"You must think me a monster, don't you Ana?"

"You tried to KILL ME!"

"If I had wanted you dead Anna, you never would have made it out of the Arctic fortress. But that's not the point. If you really want to be freed from the nano-mites you know what you must do."

"I'm not going to free you Commander and there isn't anything you can say that will change my mind."

"I'm still family, Ana."

"I have a new family now."

"Ha ha ha ha," The Commander lightly chuckled. "Do you really think the Joes will accept you as one of their own, especially after what you did?"

Ana remained silent before turning to leave. "This conversation's over."

* * *

"Are you sure these doctors know what they are doing?" Ana asked Duke nervously on the hospital bed.

"Relax Ana. These are some of the best doctors on Earth. I'll be right with you the entire time." He put a comforting hand on Anna shoulder and she tried to ease up some. The doctors entered her room shortly after and put her under anesthesia. Anna remained asleep for what seemed like hours, but then something went wrong. It felt as if her insides were being torn up. She jolted awake and was met with a great horror. The nano-mites were eating here alive! Anna looked around the room, but saw that nobody was there. She was by herself.

"Somebody help me!" She screeched at the top of her voice. Anna woke up from her nightmare completely covered in sweat.

"Ana? Are you ok?" Duke asked half-asleep.

"I'm fine Duke. Just a bad dream is all. Go back to sleep."

"Won't argue with that." He replied and then he was back out.

Ana rose from their bed and went to the closet. She input Duke's access code and took out the camouflage suit.

"I'm sorry Duke," She apologized. Then she was gone.

* * *

Scarlett sat in the control room, which controlled everything (and they meant everything), completely bored. Things had been pretty quiet on Earth ever since they took down Cobra. While she was scanning the monitors she noticed Ripcord was taking a shower and couldn't help herself. She messed with the temperature of the water.

"YAAA, COLD!" He shouted and fell down. Scarlett nearly fell out of her seat laughing. She heard the doors to security room open and said, "You're here early (thinking it was the relief shift)." Something grabbed her head from behind and slammed her face against the control panel knocking her out. Ana pushed Scarlett off the control panel and searched her for the cell keys.

"Thanks Red," Ana thanked and rose to her feet to walk off. She stopped when she heard the safety of a gun being clicked off.

"Turn around slowly and carefully, Ana." Ana did as she was told. "I knew we couldn't trust you, but Duke was so ready to believe you had changed." Scarlett kept the gun pressed right into Anna's chest.

"What are you going to do now, Scarlett? Kill me?"

"Believe me I'd like to." Suddenly Ana's hand shot out and grabbed Scarlett's gun with almost inhuman speed. She punched her in the jaw making her see stars and fall to the floor. While she fought to stay conscious she slammed her fist into the alarm.

Anna quickly ran to the control panel and punched one of the buttons before quickly exiting the room with the door automatically shutting behind her. Scarlett rose to her feet, and attempted to give chase, but the door was locked. She went to the control panel and saw that Anna had smashed the door locking mechanism.

Duke rolled out of his bed when the alarm began blasting.

"Ana!" He called out, but she was nowhere to be found. He then saw the door to his room began to automatically shut. He made a break for it and dove just in time to get out of the room. He pulled out his gun and ran for the Cell room.

* * *

Snake Eyes was busy sharpening his blades when the alarm was sounded. The door to his room slammed shut before he could reach it. Never being one to give up Snake Eyes searched his room for a way out.

* * *

Duke was running faster than he ever had in his life. He couldn't let Ana do what he believed she was going to do. He spotted her just a few hallways from the Cell Block and fired a warning shot. Ana stopped and faced Duke.

"You're going to free the Commander aren't you?" Duke asked walking closer to her, gun pointed straight at her heart.

"I'm sorry Duke, but this is the only way I can get the nano-mites out of my system." Duke unlocked the safety on his weapon when she said that. "Well doesn't this look familiar?" Ana said referencing a time when Duke had a chance to shoot her, but didn't.

"Don't make me do this, Ana,"

"If you were really going to kill me you would have done it by now."

"You're right," Duke agreed and a shot rang out. Ana looked down at her heart and was horrified by the blood that was pouring out.

"Duke," she whispered before he shot her again. He walked over to her lifeless corpse (her eyes were wide in shock). But when he bent down to close them, her hand shot out and grabbed his wrist.

"What the hell! ?" He shouted in surprise. The two of them looked down at Ana's heart and witnessed something green mending it. The nano-mites were actually healing her wound. Ana's head shot up and revealed a sadistic smile. She drove her fist into Duke's chest and sent him flying off her.

When he rose to his feet Ana stared at him with a beyond ticked off look and said, "Consider us broken up." Her hands went to her back pocket and pulled out a pulse gun. Duke fell to the floor to avoid the blast and opened fire with his own gun. She dodged every shot Matrix style. She fired her gun at the ceiling above him. Duke jumped back and avoided being crushed.

"Darn it!" He cursed punching the wall while pulling out his communicator. "Ana's on her way to free the Cobra-Commander and I've been cut off. Is there anybody that can intercept?" Duke's question was answered by the entrance to the ventilation duct above him crashing down. Snake Eyes momentarily appeared then pulled his head back up.

* * *

"Ana. To what do I owe this unexpected visit?" The Cobra-Commander asked when she came to his cell.

"It's like you said, Rex. You're still family." She unlocked both the gates for the Commander and Destro. As they exited the Cell block Snake Eyes came rushing at them both swords drawn. Ana charged him and knocked one of his swords out of his hands. She deflected his strikes with ease and kicked him in the side. Snake Eyes went down and grabbed the side of his chest.

"And you thought the nano-mites were a curse," the Commander said as they headed for the hanger. As they began to board one of the Joes jets, Duke ran into the hangar shouting, "ANA!" He fired all the bullets in his gun, but wasn't at a close enough range. Rexx pulled out a sniper's rifle from the jet and shot Duke in the leg. When he went down he aimed the gun at his head.

"Good bye old friend." The Commander said and fired. It all happened in slow motion; the bullet flew at Duke, who was helpless to dodge. But just when the bullet was about to end his life Snake Eyes appeared from out of nowhere and deflected the bullet with his sword.

"What's that thing made of?" Duke wondered.

They were too late, however, to stop the Cobra team from escaping.

**A/N: Yes it is because of the nano-mites that Ana has developed some superhuman abilities. Hope you liked****this.**


	2. Aftermath

**A/N: Since a few people have asked I've decided after a long absence to continue this story. This update is short, but should be satisfying. Think of it as a teaser. Anyway, enjoy.**

The stolen G.I. Joe Jet rocketed through the night sky. Onboard, Ana merely looked out the window. Her hand placed over her heart. She honestly couldn't believe that Duke had shot her! Meanwhile a conversation was being held between the Cobra Commander and Destro up in the cockpit.

"Not that I have a problem with her freeing us or anything, but why did Ana help us? I thought she wasn't under your control anymore." Destro questioned looking back towards Ana, who was still lost in thought.

"Have you ever heard the age old expression 'hell hath no fury like a women scorned'?" The Commander asked with a light chuckle.

"Well, yes. Why exactly?"

"Ana loved Duke; more so than I have ever seen her love any man before. No doubt she still does love him. When he shot her, my only guess is that Ana's heart was shattered. If my guess is correct that sudden shock mixed in with the nano-mites still in her system somehow messed with her mind. It's quite possible she will never be the same person ever again. Which is a big plus in our case wouldn't you think?"

"I guess you are right."

"So boys," Ana began entering the cockpit. "What's our next course of action?"

"We're heading for Washington." The Commander revealed.

"Why there of all places? Won't people be looking for us there?" Ana asked perplexed.

"It's all part of my plan, Ana. The nano-mites were never intended to be successful. I was willing to bet money that the Joes' would accomplish in destroying them. They've served their purpose now. Once we arrive in Washington, the real fun begins. HAHAHAHAHAHAHAH!"

_

**One Week later**

Duke was pummeling the punching bag like it was the last thing on Earth to hit. He had never been so pissed before in his entire life. Not even when he found out the Rex was alive and working with Cobra. He couldn't believe that Ana betrayed him; and that look in her eyes when she came back to life. It actually scared him for a moment. Duke was so lost in his own world that he didn't hear Ripcord enter the gym.

"Hey Duke!"

Duke was so caught off guard by his friend's sudden appearance that he wound up breaking the punching bag off. Ripcord sighed and pulled out a cell phone.

"Hey Scarlett. Better get a new punching bag. Duke broke it…again."

"That's the fourth one this week! These punching bags don't come cheap!" Scarlett complained while hanging up. Ripcord took a deep breath and approached Duke.

"Hey Ripcord," Duke greeted. "What happened to you?" He asked observing the bandages wrapped around his forehead.

"Fell down while I was in the shower. Someone keeps messing with the shower temperatures," He explained while giving a small laugh hoping Duke would laugh as well. Duke, however, remained silent and turned his attention back to the wall.

"So are you feeling any better?" Ripcord uneasily asked not wanting to end up like the punching bag.

"Do I look ok, Rip?" Duke responded bracing himself against the gym walls. "I loved her and she betrayed me. Who knows what the hell Rex will do now that he's free? Ana will always be the Baroness to me now and forever. And I swear to you Ripcord. Next time I see her I'm putting a bullet in her brain!" Duke lasts comment made Ripcord jump back. He' never seen Duke this angry or upset before. He was hurting and there wasn't anything he could do about it. Ripcord was about to make a second attempt to get through to Duke when the base's sirens started to blast. Duke and Ripcord ran to the mission debriefing room, which was already filled with several other Joes.

"What's going on?" Ripcord asked approaching Scarlett from behind.

"Your guess is as good as mine," Scarlett replied just as confused as everyone else. Everyone went silent as General Hawk entered and walked to the center of the room. He took a long pause followed by a heavy sigh before he began to speak to the other Joes.

"My fellow G.I. Joes. It has been an honor and a privilege to fight by all of you. To preserve peace in the world. Now it is with a heavy heart and my deepest regrets that I must inform you that those days have come to an end."

"Wait, are you retiring or something?" Duke asked.

"I wish it was that simple Duke, but as of O twelve hundred hours G.I. Joe has been officially disbanded by the President of the United States.

**To Be Continued…**

**A/N: Nice cliffhanger huh? What will the Joes do now that they've been shut down? And more importantly what will the Cobra Commander do now that there is no one left to oppose him? Only one way to find out. Please review.**


	3. GI Joe Disbanded! ?

**A/N: Sorry about the wait readers. Enjoy chapter three!**

"You want to run that by us again?" Scarlet asked.

"What do you mean we're disbanded! ?" Duke yelled.

"I wish I could explain it, but I can't. The President just called and informed me that we were disbanded."

"Is he out of his mind! ?" Breaker shouted.

"Damn right he's out of his mind!" Heavy Duty yelled. "We've done more than our fair share of keeping this world safe and secure!"

"I'm sorry team, but there really isn't anything that I can do" General Hawk regretfully informed them.

"This doesn't make any sense," Ripcord said. "We saved some of Earth's major cities. Sure Paris wasn't a complete success, but they can't hold that against us forever."

"Again, I can't explain it. The president wasn't exactly specific on his reason for disbanding us. He just said that we were no longer needed and to leave it at that."

"So where are we supposed to go from here?" Duke asked. "Given how we don't officially exists and all it's not like we can just rejoin whatever branch of the military we left for this."

"The President said that we will all be compensated for our services to the United States, but that this is the end of G.I. Joe and that nothing will change his mind."

"Didn't you tell him about the Cobra Commander escaping from his cell along with Destro? Those two being back on the loose alone should be more than enough reason for us to stay together."

"The President ended the call before I could inform him of that and all further attempts to reach him have been met with failure," he told Duke. He sighed and continued. "The base is to be shut down in one month's time. It is unknown what will become of it. I truly am sorry that this is how things must end team and I wish you all the best of luck wherever it is that you end up." The General gave them all a salute, which the team returned. "For the last time you are all dismissed." It took the team a good few seconds to actually start exiting the debriefing room. They were all truly shocked at the bombshell the General dropped on them. It was too much to take in at once.

"This just can't be happening. It can't!" Duke shouted punching one of the walls.

"Take it easy there, Duke," Ripcord tried to calm him down.

"We're all shocked too, but getting upset isn't going to change anything," Scarlett said.

"I know," he sighed. "But there has to be something… some reason why the president would disband us and not even say why. What if the Commander is behind this? He could've threatened the President to disband us that way there'd be no one else on Earth that could oppose him, Destro, and the Baroness."

"You mean Ana?" Ripcord asked.

"Don't use that name!" He snapped at his friend.

"Sorry Duke. Sorry," he apologized with his hands up.

"Sorry. I didn't mean to snap at you. I'm going to get to the bottom of this one way or another."

"What are you planning on doing?" Breaker questioned him.

"I'm taking a trip up to Washington. Get the answers straight from the horses' mouth," Duke said already heading back to his room. Any of you want to come?" He asked. No one responded at first, but then Ripcord stepped forward.

"I'm just as curious as you are so, I'm in."

"So am I," Scarlet said.

"You can count me in," Heavy Duty replied.

"I'll go along as well, but if you do anything stupid you're on your own. We've already been banned from Paris and I'd like to not be banned from the Washington D.C.," Breaker said.

* * *

**Washington D.C.**

Anna spun the throwing star in her hand and threw it to the other side of the room hitting the picture of Scarlet dead in the center.

"Nice throw sister. Storm Shadow would be proud," The Cobra Commander said entering her room.

"Glad you approve. Now would you mind telling me just why you've kept us all confined in the White House? Won't people think to raise an alarm if we're spotted?"

"It's all been taken care of Ana. The 'President' has ensured that no one will show up in this part of the White House. He also has people working round the clock on our new base so soon you won't have to be trapped here any longer."

"So what exactly is your next big plan?" Ana asked him.

"That will be revealed in due time, Ana," he cryptically answered and then his communicator went off. "What is it?"

"You're not going to believe this. Some of the Joes have arrived at the White House and have demanded to see me," the Cobra member pretending to be the President said.

"Send them in," the Commander ordered him.

"Yes sir." The Commander pulled out a small remote and pressed it. A giant screen appeared from behind the wall and switched on to reveal the President's office.

* * *

"Good afternoon, sir," Duke greeted the President.

"Good afternoon Joes. What can I do for you all?"

"You can tell us the reason why you had us disbanded," Duke said.

"I told the General that you simply were no longer needed. Surely he told you all that."

"There has to be a bigger reason than we aren't needed anymore," Duke said putting his hands on the President's desk. Ripcord had o pull him back a little.

"He's right," Scarlett agreed.

"You should also know that the Cobra Commander escaped from our holding facility not too long ago," Breaker said.

"He what?" The President asked sounding surprised.

"Baroness betrayed us. She set him and Destro free and they escaped in one of our jets," Heavy Duty informed him.

"Well let me assure you that I will have everyone working into the night to track those three down. However, you won't be needed."

"Why not! ?" Duke shouted slamming his fist on the desk.

"Because though you've proven yourselves capable you've also shown that you can be beaten by Cobra. Not only did they manage to steal back the nano-mites from you, but they destroyed the Eifel Tower, and nearly wiped Washington D.C. off the map. It was only by the grace of God that you managed to succeed in stopping them, but I can't risk another incident like Paris ever occurring again."

"You can't hold that over our heads forever," Ripcord said also getting in the President's face.

"I'm sorry, but as President of the United States I must make decisions that are in America's best interest." He pressed a button on the intercom on his desk. "Security," He said. The security stepped into the office. "Please escort our guests out," he requested. The security team nodded and led the frustrated Joes out of the White House.

* * *

"That went well," Breaker said once they were thrown outside.

"Something is up though. I can feel it," Duke said. He was going to find out just what was up with the President even if it killed him.

* * *

**Later that day in Washington D.C.**

"What am I supposed to do now?" Scarlett thought. Since she and the guys had nothing better to do for the rest of the day they decided to enjoy the rest of their time in Washington D.C. She was now in a deserted gym doing sit-ups to clear her head. Being a Jo was all she'd known and she really didn't know what she could do if Duke couldn't figure out what was up with the President. Something did seem odd about him, but she could think of what. As she continued to exercise another person entered the gym. "197, 198, 199, 200," She finished and sprawled out on the floor.

"Very impressive Red," she heard a familiar voice call out.

"Baroness; what are you doing here?" She asked jumping onto her feet.

"Heard you and the rest of the Joes were disbanded; how unfortunate," she said in a fake sad tone.

"What do you want?" Scarlett asked as Ana walked up to her.

"We never got a chance to finish our little fight during the ambush," Ana said stopping an inch in front of Scarlett.

"You're a little close," Scarlett said not backing away from her.

"I'm sorry. Is this uncomfortable for you?" Ana asked smirking.

"A little," Scarlett replied tilting her head with her own smirk. Ana lashed out at Scarlett, who just managed to stop Ana from stabbing her in the chest. "You'll have to be quicker than that," she said keeping the knife at bay.

"You should know that I trained under Storm Shadow."

"Funny; I trained with the guy that killed him," Scarlett countered and knocked Anna's knife out of her hand. Scarlett launched her foot into Anna's gut knocking her back a little. Ana cracked her knuckles and rushed Scarlett. She blocked Ana's punch and hit her in the chest. Ana recovered and ducked Scarlett's left hook. She directed a kick into Scarlett's stomach knocking her off her feet and sent her sliding across the floor.

"Had enough?" Ana asked.

"I'm just getting started," Scarlett replied and went back on the attack.

**A/N: Scarlet vs. Ana round 2. Fight! On another note, what could the Commander be planning in that evil mind of his and with the Joes disbanded who can stop him now? Keep reading to find out. See ya!**


End file.
